7WMO

A novel chemical derivative(92) of THRB agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Highly Selective and H435R-Sensitive Thyroid Hormone Receptor beta Agonist.

Li, Q.Yao, B.Zhao, S.Lu, Z.Zhang, Y.Xiang, Q.Wu, X.Yu, H.Zhang, C.Li, J.Zhuang, X.Wu, D.Li, Y.Xu, Y.

(2022) J Med Chem 65: 7193-7211

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00144
  • Primary Citation of Related Structures:  
    7WLX, 7WMG, 7WMH, 7WMJ, 7WML, 7WMN, 7WMO

  • PubMed Abstract: 

    The design and development of agonists selectively targeting thyroid hormone receptor β (TRβ) and TRβ mutants remain challenging tasks. In this study, we first adopted the strategy of breaking the "His-Phe switch" to solve two problems, simultaneously. A structure-based design approach was successfully utilized to obtain compound 16g , which is a potent TRβ agonist (EC 50 : 21.0 nM, 85.0% of the maximum efficacy of 1 ) with outstanding selectivity for TRβ over TRα and also effectively activates the TRβ H435R mutant. Then, we developed a highly efficient synthetic method for 16g . Our serials of cocrystal structures revealed detailed structural mechanisms in overcoming subtype selectivity and rescuing the H435R mutation. 16g also showed excellent lipid metabolism, safety, metabolic stability, and pharmacokinetic properties. Collectively, 16g is a well-characterized selective and mutation-sensitive TRβ agonist for further investigating its function in treating dyslipidemia, nonalcoholic steatohepatitis (NASH), and resistance to thyroid hormone (RTH).


  • Organizational Affiliation

    Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Beta-2 of Thyroid hormone receptor beta260Homo sapiensMutation(s): 0 
Gene Names: THRB
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
PHAROS:  P10828
GTEx:  ENSG00000151090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10828
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 211Homo sapiensMutation(s): 0 
Gene Names: SRC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9IW (Subject of Investigation/LOI)
Query on 9IW

Download Ideal Coordinates CCD File 
C [auth A]2-[[1-ethoxy-7-[4-(3-fluoranyl-5-methoxy-phenyl)carbonyl-2,6-dimethyl-phenoxy]-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid
C30 H27 F N2 O8
DLRMKPITDQZMBN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.558α = 90
b = 106.558β = 90
c = 56.681γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770814

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description